Structure of PDB 8c5s Chain A

Receptor sequence

>8c5sA (length=924) Species: 559292 (Saccharomyces cerevisiae S288C)

INFFEIYNSLPTLEEKKAFESALNIFNQDRQKVLENRATEAARERWKHDF
EEAKARGDISIEKNLNVKLWKWYNEMLPLVKEEINHCRSLLSEKLSDKKG
LNKVDTNRLGYGPYLTLIDPGKMCVITILELLKLNSTGGVIEGMRTARAV
ISVGKAIEMEFRSEQVLKKILWPQSIRARIGSVLISMLIQVAKVSVQGVD
PVTKAKVHGEAPAFAHGYQYHNGSKLGVLKIHKTLIRQLNGERLIASVQP
QLLPMLVEPKPWVNWRSGGYHYTQSTLLRTKDSPEQVAYLKAASDNGDID
RVYDGLNVLGRTPWTVNRKVFDVVSQVWNKGEGFLDIPGAQDEMVLPPAP
PKNSDPSILRAWKLQVKTIANKFSSDRSNRCDTNYKLEIARAFLGEKLYF
PHNLDFRGRAYPLSPHFNHLGNDMSRGLLIFWHGKKLGPSGLKWLKIHLS
NLFGFDKLPLKDRVAFTESHLQDIKDSAENPLTGDRWWTTADKPWQALAT
CFELNEVMKMDNPEEFISHQPVHQDGTCNGLQHYAALGGDVEGATQVNLV
PSDKPQDVYAHVARLVQKRLEIAAEKGDENAKILKDKITRKVVKQTVMTN
VYGVTYVGATFQIAKQLSPIFDDRKESLDFSKYLTKHVFSAIRELFHSAH
LIQDWLGESAKRISKSIRLDVDEKSFKNGNKPDFMSSVIWTTPLGLPIVQ
PYREESKKQVETNLQTVFISDPFAVNPVNARRQKAGLPPNFIHSLDASHM
LLSAAECGKQGLDFASVHDSYWTHASDIDTMNVVLREQFIKLHEVDLVLR
LKEEFDQRYKNYVKIGKLKRSTDLAQKIIRIRKDLSRKLGRSTTLADEIY
FEKKRQELLNSPLIEDRNVGEKMVTTVSLFEDITDLDALELSGMSVLLPL
RLPEIPPKGDFDVTVLRNSQYFFS

3D structure

• PDB: 8c5s Structures illustrate step-by-step mitochondrial transcription initiation
• Chain: A
• Resolution: 3.75 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	Y640 N642 G643 K645 R780 K1081	Y220 N222 G223 K225 R360 K661
BS02	dna	A	S521 T522 G523 G524 R530 Y638 S644 K645 G647 S794 S798 R827 Y831 P835 T1019 Y1022 G1023 T1025 V1027 G1028 Y1122 Q1129 Q1135 T1136 V1137 F1138 R1151 R1152 P1159 H1163	S136 T137 G138 G139 R145 Y218 S224 K225 G227 S374 S378 R407 Y411 P415 T599 Y602 G603 T605 V607 G608 Y702 Q709 Q715 T716 V717 F718 R731 R732 P739 H743
BS03	rna	A	R829 L840 R846 M1018 Y1022 H1163 H1188	R409 L420 R426 M598 Y602 H743 H768

Gene Ontology

Molecular Function

• GO:0001018 mitochondrial promoter sequence-specific DNA binding
• GO:0003677 DNA binding
• GO:0003896 DNA primase activity
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity

Biological Process

• GO:0000002 mitochondrial genome maintenance
• GO:0006269 DNA replication, synthesis of primer
• GO:0006351 DNA-templated transcription
• GO:0006390 mitochondrial transcription

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0034245 mitochondrial DNA-directed RNA polymerase complex
• GO:0042645 mitochondrial nucleoid
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8c5s, PDBe:8c5s, PDBj:8c5s
• PDBsum: 8c5s
• PubMed: 37821701
• UniProt: P13433|RPOM_YEAST DNA-directed RNA polymerase, mitochondrial (Gene Name=RPO41)